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Started on gn1 package

Added python2-numarray 1.5.2
gn-stable
pjotrp 5 years ago
parent
commit
d1c83a621f
3 changed files with 89 additions and 3 deletions
  1. +10
    -3
      README.md
  2. +51
    -0
      gn/packages/bioinformatics.scm
  3. +28
    -0
      gn/packages/python.scm

+ 10
- 3
README.md View File

@@ -30,7 +30,6 @@ Install slurm with
~/.guix-profile/sbin/slurmd -C -D
ClusterName=(null) NodeName=selinunte CPUs=4 Boards=1 SocketsPerBoard=1 CoresPerSocket=2 ThreadsPerCore=2 RealMemory=7890 TmpDisk=29909


## Module system

Install the module envirmonment with
@@ -43,6 +42,14 @@ Install the module envirmonment with
VERSION=3.2.10
DATE=2012-12-21

## python2-numarray 1.5.2

Install the module envirmonment with

git clone https://github.com/genenetwork/guix-bioinformatics.git
export GUIX_PACKAGE_PATH=$PWD/guix-bioinformatics/
guix package -i python2-numarray

## Common Workflow Language (CWL)

Install the common workflow language tool cwltool with
@@ -54,12 +61,12 @@ Install the common workflow language tool cwltool with
cwtool --version
1.0.20150916041152

# Packages moved from here to main line GNU Guix

## LLVM D compiler

The LLVM D compiler was added to GNU Guix main stream!

Install with

guix package -i ldc
## R/qtl


+ 51
- 0
gn/packages/bioinformatics.scm View File

@@ -22,6 +22,7 @@
#:use-module (gnu packages databases)
#:use-module (gnu packages cpio)
#:use-module (gnu packages file)
#:use-module (gnu packages graphviz)
#:use-module (gnu packages java)
#:use-module (gnu packages linux)
#:use-module (gnu packages machine-learning)
@@ -156,6 +157,56 @@ confidence region for the location of a putative QTL.")
(license license:gpl2)))


(define-public genenetwork1
(let ((commit "d622c803b"))
(package
(name "genenetwork1")
(version (string-append "1.0-" commit ))
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/pjotrp/genenetwork.git")
;; (url "https://github.com/pjotrp/genenetwork.git")
(commit commit)))
(file-name (string-append name "-" commit))
(sha256
(base32
"09hvy9mf4dnmkb8qg49viffzrxk53m2kr4r955m84dxaa5pdrjha"))))
(propagated-inputs `(
("python" ,python-2) ;; probably superfluous
("r" ,r)
))
(inputs `(
;; graphviz-2.22.2 htmlgen json numarray-1.5.2 piddle PIL pp-1.5.7 pyx pyXLWriter svg
("mysql" ,mysql)
("nginx" ,nginx)
("graphviz" ,graphviz)
; ("python2-jinja2" ,python2-jinja2)
; ("python2-sqlalchemy" ,python2-sqlalchemy)
; ("python2-setuptools" ,python2-setuptools)
; ("python2-scipy" ,python2-scipy)
;; looks like python-numarray is not needed
; ("python2-numpy" ,python2-numpy)
; ("python2-pandas" ,python2-pandas)
; ("python2-passlib" ,python2-passlib)
; ("python2-redis" ,python2-redis)
; ("python2-requests" ,python2-requests)
; ("python2-simplejson" ,python2-simplejson)
; ("python2-pyyaml" ,python2-pyyaml)
;; python-yolk is not needed
("python2-pil" ,python2-pil)
("plink" ,plink) ;; gn1
; ("r-qtl" ,r-qtl)
))
(build-system python-build-system)
(arguments
`(#:python ,python-2
#:tests? #f)) ; no 'setup.py test'
(home-page "http://genenetwork.org/")
(synopsis "Full genenetwork services")
(description "Genenetwork installation sumo.")
(license license:agpl3+))))

(define-public genenetwork2
(let ((commit "9e9475053"))
(package


+ 28
- 0
gn/packages/python.scm View File

@@ -175,3 +175,31 @@ powerful language for representing information.")

(define-public python2-shellescape
(package-with-python2 python-shellescape))

(define-public python2-numarray
(package
(name "python2-numarray")
(version "1.5.2")
(source
(origin
(method url-fetch)
(uri (string-append
;; http://sourceforge.net/projects/numpy/files/Old%20Numarray/1.5.2/numarray-1.5.2.tar.gz/download
"mirror://sourceforge/numpy/numarray-" version ".tar.gz"
))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"0x1i4j7yni7k4p9kjxs1lgln1psdmyrz65wp2yr35yn292iw2vbg"))))
(build-system python-build-system)
;; (native-inputs
;; `(("python-setuptools" ,python-setuptools)))
(arguments
`(#:python ,python-2
#:tests? #f)) ; no 'setup.py test' really!
(home-page "http://www.numpy.org/")
(synopsis "Numerical library array processing of numbers, strings, records and objects")
(description
"Numarray is an array processing package designed to efficiently manipulate large multi-dimensional arrays. Numarray is modelled after Numeric and features c-code generated from python template scripts, the capacity to operate directly on arrays in files, and improved type promotions. Numarray provides support for manipulating arrays consisting of numbers, strings, records, or objects using the same basic infrastructure and syntax. Numarray is now part of the
numpy package, though some legacy software still uses the older versions.")
(license license:gpl2))) ; actualy PyRAF http://www.stsci.edu/resources/software_hardware/pyraf/LICENSE

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